Transforming X-ray diffraction data obtained from protein crystals into three-dimensional structure requires the determination of the X-ray phases. Traditionally, phase determination necessitates the inclusion of heavy-atoms in the protein crystals. Mass spectrometry provides a practical means of analyzing incorporation of heavy atoms into proteins. No other methods have been available. We investigated of the incorporation of mercury into proteins using MALDI- and ESI-MS. Mercurating reagents were chosen because of their widespread use as heavy-atom reagents in protein crystallography. We found dramatic differences between the MALDI and ESI of mercurated protein. Electrospray ionization yielded the most accurate, quantitative results, although samples required extensive clean up. MALDI-MS yielded more rapid information than ESI-MS since sample clean-up requirements were minimal. However, while ESI-MS showed nearly 100% mercury derivatization of a given mer cury-deriv atized protein, MADLI-MS consistently and often dramatically underestimated the extent of derivatization. The anomalous MALDI effects were dependent on the MALDI matrix, the matrix solution pH and on the type of mercurating reagent. We attribute much of the distinctions between the results to the differences inherent to the energetically "cooler" electrospray process and the "hotter" MALDI process. A paper describing this work is in preparation.